Alignments for a candidate for fadA in Thermodesulforhabdus norvegica DSM 9990

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Thermodesulforhabdus norvegica DSM 9990

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_093392702.1 BM091_RS00785 thiolase family protein

Query= metacyc::MONOMER-13468
         (393 letters)



>NCBI__GCF_900114975.1:WP_093392702.1
          Length = 399

 Score =  397 bits (1021), Expect = e-115
 Identities = 213/395 (53%), Positives = 277/395 (70%), Gaps = 6/395 (1%)

Query: 3   EVVIVSAVRTAIGSFGGTLKDVSAVDLGAIVIKEAVKRAGIKPEQVDEVIFGNVIQAGVG 62
           ++V+V  VRTAIG FGGTLKDV A  L A V+K  V R GI P  +D++I G+ +Q    
Sbjct: 6   DIVLVGGVRTAIGRFGGTLKDVRASQLAAHVMKAVVDRTGIDPGMLDDIIAGDCLQNADE 65

Query: 63  QSLARQSAVYAGLPVEVPAFTVNKLCGSGLRTVSLAASLISNGDADTIVVGGSENMSASP 122
            + AR +A+ AG PV VPA+T+ + C S ++ V+ AA  I  GDA+ I+V G E+MS++P
Sbjct: 66  ANTARTAALLAGFPVHVPAYTIQRQCSSSMQAVASAAQAIKAGDAELIMVVGVESMSSAP 125

Query: 123 YLIPKARFGYRMGEAKIYDAM---LHDGLIDSFNNYHMGITAENIAEKWGITREDQDKFA 179
           Y + KAR+G R+   +  DA+   LH G         MG TAEN+AEK+ I+R +QD+ A
Sbjct: 126 YYLSKARWGMRLQHQECTDALWEALHSGSRLLGRPMIMGETAENLAEKYNISRREQDEVA 185

Query: 180 LASQQKAEAAIKAGKFKDEIVPVTVKMKKKEV-VFDTDEDPRFGTTIETLAKLKPAFKRD 238
           LAS QKAEAAIKAGKFKDEIVP+ VK  K +V VFD DE PRFG T+E LAKL P FK++
Sbjct: 186 LASHQKAEAAIKAGKFKDEIVPIEVKGPKGQVIVFDQDEHPRFGLTLEDLAKLPPVFKKN 245

Query: 239 GTGTVTAGNSSGINDSSAALILMSADKAKELGVKPMAKYVDFASAGLDPAIMGYGPYYAT 298
           GT  VTAGNSSGIND +AA ++ +  KA+ELG++P+ + V  A AG++P  MGYGP  AT
Sbjct: 246 GT--VTAGNSSGINDGAAAALITTRRKARELGLEPLVRIVATAVAGVEPEFMGYGPVPAT 303

Query: 299 KKVLAKTNLTIKDFDLIEANEAFAAQSIAVARDLEFDMSKVNVNGGAIALGHPVGCSGAR 358
           +KVL K  +T+K+ +LIE NEAFAAQ IA  R L  D S  NVNG  I+LGHPVGC+G R
Sbjct: 304 QKVLKKAGMTLKNVELIELNEAFAAQYIACERGLGIDRSITNVNGSGISLGHPVGCTGLR 363

Query: 359 ILVTLLHEMQKRDAKKGLATLCIGGGQGTAVVVER 393
           I+++L +EM++RD   GLATLC+GGG G A +V R
Sbjct: 364 IIISLAYEMKRRDLNVGLATLCVGGGMGMATIVAR 398


Lambda     K      H
   0.316    0.133    0.369 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 439
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 393
Length of database: 399
Length adjustment: 31
Effective length of query: 362
Effective length of database: 368
Effective search space:   133216
Effective search space used:   133216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_093392702.1 BM091_RS00785 (thiolase family protein)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01930.hmm
# target sequence database:        /tmp/gapView.3696786.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-146  474.0   3.1   1.9e-146  473.8   3.1    1.0  1  NCBI__GCF_900114975.1:WP_093392702.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900114975.1:WP_093392702.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.8   3.1  1.9e-146  1.9e-146       2     384 ..      10     396 ..       9     397 .. 0.98

  Alignments for each domain:
  == domain 1  score: 473.8 bits;  conditional E-value: 1.9e-146
                             TIGR01930   2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesv 74 
                                           v++vRt+ig++gg+lk+++a++L+a+v+k++++r+g+dp  +d++i G  lq++++an+aR+aal ag+p +v
  NCBI__GCF_900114975.1:WP_093392702.1  10 VGGVRTAIGRFGGTLKDVRASQLAAHVMKAVVDRTGIDPGMLDDIIAGDCLQNADEANTARTAALLAGFPVHV 82 
                                           89*********************************************************************** PP

                             TIGR01930  75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl... 144
                                           pa+t++r+C+S++qAva+aaq+ikaG+a+++++ GvEsmS++p++l+++  r++++l++++  d+l + l   
  NCBI__GCF_900114975.1:WP_093392702.1  83 PAYTIQRQCSSSMQAVASAAQAIKAGDAELIMVVGVESMSSAPYYLSKA--RWGMRLQHQECTDALWEALhsg 153
                                           ***********************************************98..8999999999999888888999 PP

                             TIGR01930 145 ...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegi 211
                                                  + mgetAenla+ky+isR+eqDe al+Shqka++Ai++gkfkdeivp+evkg      v+++De++
  NCBI__GCF_900114975.1:WP_093392702.1 154 srlLGRPMIMGETAENLAEKYNISRREQDEVALASHQKAEAAIKAGKFKDEIVPIEVKGPkgqVIVFDQDEHP 226
                                           99966789**************************************************999988999****** PP

                             TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemgl 284
                                           r ++tle+LakL+p+fk+ +g tvtAgNss++nDGAaa+l++++++a+elgl+pl riv++avagv+pe mg+
  NCBI__GCF_900114975.1:WP_093392702.1 227 RFGLTLEDLAKLPPVFKK-NG-TVTAGNSSGINDGAAAALITTRRKARELGLEPLVRIVATAVAGVEPEFMGY 297
                                           ****************95.9*.6************************************************** PP

                             TIGR01930 285 gpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltll 357
                                           gpvpA++k+Lkkag+++++++l+E+nEAFAaq++a+e+ lg +d++  NvnG+ i+lGHP+G++G ri+++l+
  NCBI__GCF_900114975.1:WP_093392702.1 298 GPVPATQKVLKKAGMTLKNVELIELNEAFAAQYIACERGLG-IDRSITNVNGSGISLGHPVGCTGLRIIISLA 369
                                           *****************************************.88***************************** PP

                             TIGR01930 358 keLkergkkyGlatlCvggGqGaAvil 384
                                           +e+k+r+ ++GlatlCvggG+G+A+i+
  NCBI__GCF_900114975.1:WP_093392702.1 370 YEMKRRDLNVGLATLCVGGGMGMATIV 396
                                           *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (399 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.68
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources